We report on the fabrication of long-range ordered arrays of Au nanocrystals (sub-50 nm range) on top of manganite (La2/3Sr1/3MnO3) thin films achieving area densities around 2 × 1010 gold nanocrystals per cm2, well above the densities achievable by using conventional nanofabrication techniques. The gold–manganite interface exhibits excellent conduction properties. Long-range order is achieved by a guided self-assembling process of Au nanocrystals on self-organized pit-arrays acting as a template for the nucleation of gold nanocrystals. Self-organization of pits on the manganite film surface promoted by the underlying stepped SrTiO3 substrate is achieved by a fine tuning of the growth kinetic pathway, taking advantage of the unusual misfit strain relaxation behaviour of manganite films.